Habitats Show More Impacts Than Host Species in Shaping Gut Microbiota of Sympatric Rodent Species in a Fragmented Forest

Teng, Yuwei; Yang, Xifu; Li, Guoliang; Zhu, Yushan; Zhang, Zhibin

doi:10.3389/fmicb.2022.811990

Cited by 10 publications

(14 citation statements)

References 76 publications

(95 reference statements)

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“…Our study contributes to bridging this gap by showing that degradation of the host habitat through land-use changes can indeed induce a shift in the composition of microbial communities, and even have a positive effect, on the overall bacterial species richness associated with insects. This is in clear contradiction with our original expectations that degradation of the host habitat would also be detrimental to their associated microbial diversity and functionality (McManus et al 2021, Teng et al 2022). One possible explanation for these results is that habitat degradation in the Åland meadow network is not strong enough to lead to microbial erosion in the insect species studied.…”

Section: Discussioncontrasting

confidence: 97%

“…For many species, the composition of the microbiota, and especially that of the gut microbiota, is representative of their diet (McManus et al 2021). Recently, Teng et al (2022) suggested that differences in the gut microbiota associated with populations from three rodent species were linked to changes in diets between populations. The animals from farmlands, where food diversity is high, hosted the most species- rich microbiota (Teng et al 2022).…”

Section: Discussionmentioning

confidence: 99%

“…Recently, Teng et al (2022) suggested that differences in the gut microbiota associated with populations from three rodent species were linked to changes in diets between populations. The animals from farmlands, where food diversity is high, hosted the most species- rich microbiota (Teng et al 2022). In Åland, both the adult weevils and the caterpillars likely remain within their own meadow (Smith et al 2021), where the weevil M. pascuorum is a specialist herbivore of P. lanceolata , feeding on the leaves as adults, and on the seeds as larvae (Nieminen and Vikberg 2015), while, the caterpillars of M. cinxia can feed on a second host plant Veronica spicata , which was not recorded within our selected meadows (Hanski et al 2002, Hanski 2011).…”

Section: Discussionmentioning

confidence: 99%

“…Although habitat degradation is often associated with negative effects on macro-biodiversity level (Soh et al 2019, Teng et al 2022, Uhl et al 2021), the study of the impact of such Anthropogenic changes on microbial communities associated with species (ie. symbioses) remains scarce (Hom and Penn 2021).…”

Section: Discussionmentioning

confidence: 99%

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Species-associated bacterial diversity increases along a gradient of habitat degradation

Hanhimäki,

Linna,

Beraldo

et al. 2024

Preprint

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Alterations of microbial communities have evident impacts on development, digestion, fecundity, metabolism, immunity, and diverse other biological functions of their hosts. Yet, the factors affecting microbial communities associated with wild species often remain uncharacterized. For example, the impact of the hosts habitat degradation due to anthropogenic activities has received little attention, which contrasts with the large literature showing how such habitat degradation is at least partly responsible for the on-going global patterns of macro-biodiversity erosion. Here, we use metacommunities of herbivorous insect species specialized in feeding on Plantago lanceolata in the fragmented landscape of the Aland Islands, Finland, as a model system to test whether and how bacterial communities associated with wild species change along a gradient of habitat degradation. We evaluated microbial species diversity and community composition in two sympatric insect species sampled from local meadow habitats with various levels of human disturbance within or around these habitats (e.g. forests, roads, agriculture fields, buildings). Counter to our expectations, we found that bacterial diversity can increase with habitat degradation, with individuals from more degraded habitats hosting more rare bacterial species. In contrast, as the dominant microbial species remain similar across habitats, the community composition and function of the microbiota persist under habitat degradation. In this system, the strength of human activities might induce changes in habitat heterogeneity rather than changes in overall habitat quality, thus allowing local insects to encounter and host more rare microbes rather than trigger local microbial extinction.

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Section: Discussioncontrasting

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Species-associated bacterial diversity increases along a gradient of habitat degradation

Hanhimäki,

Linna,

Beraldo

et al. 2024

Preprint

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“…The few studies that investigated GM variations within host communities led to incongruent patterns with either a stronger impact of host phylogeny over habitats on GM assembly (e.g. Knowles et al, 2019) or the opposite (Teng et al, 2022). Therefore, gathering more data on the relationships between urbanization, host community assembly and their GM remains critical in the domain of urban ecology (Verrelli et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Effects of forest urbanization on the interplay between small mammal communities and their gut microbiota

Bouilloud,

Galan,

Pradel

et al. 2023

Preprint

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Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid and abrupt changes. One possible explanation for differential adaptative abilities between these species is that the microbiome may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under such anthropic perturbations, the microbiota composition of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness, potentially causing local extirpation. The links between the impact of urbanization on host communities and their gut microbiota have only been scarcely explored. In this study, we tested the hypothesis that the gut microbiota (GM) could play a role in host adaptation to urban environments. We addressed this question by studying several species of small terrestrial mammals sampled in forested areas along a forested gradient of urbanization (from rural forests to urban parks) during 2020 fall. The gut was collected and bacteria were described using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM. We analyzed these changes in terms of the presence and abundance of taxa and their putative functions to decipher the processes underlying these changes. We found that urbanization had marked impacts on small mammal communities and their GM, either directly or indirectly depending on small mammal species categories. The urban dweller species had a lower taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, which could indicate dysbiosis in these urban species. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite potential dysbiosis. Urbanization could also impact the diversity and taxonomic composition of GM in urban adapter species. However, their functional diversity and composition remained relatively stable. This observation can be explained by functional redundancy, where certain taxa express the same function. This could explain the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedback loops between the gut microbiota and the host species within communities, enabling rapid and flexible adaptation.

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Phylosymbiosis in Seven Wild Fish Species Collected Off the Southern Coast of Korea: Skin Microbiome Most Strongly Reflects Evolutionary Pressures

Han,

Yu,

Kang

et al. 2024

Microb Ecol

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Phylosymbiosis is defined as the relationship in which the microbiome recapitulates the phylogeny of the host and has been demonstrated in a variety of terrestrial organisms, although it has been understudied in fish, the most phylogenetically diverse vertebrate. Given that the species-specificity of fish microbiomes was detected in multiple body parts and differed by body parts, we assumed that the phylogenetic reflection of the microbiome would differ across body parts. Thus, we analyze the difference of phylosymbiotic relationships in the microbial communities found in three body parts (skin, gills, and intestine) of seven wild fish species from four families (Labridae, Sebastidae, Sparidae, and Rajidae) via 16S rRNA gene amplicon sequencing. Fishes were purchased at Docheon port market in Tongyeong City, Korea and were transported to nearby research institutes for aliveness. Mantel tests using dissimilarity values of microbiomes and hosts' divergence times showed that the differences in microbial communities in all three body parts were related to the hosts' divergence time. This pattern was the most pronounced in the skin. Furthermore, fishes from the same family showed similar bacterial compositions on their skins and gills, with clear differences depending on the family, with the exception of Labridae. These results suggest that the skin microbiome is particularly vulnerable to evolutionary pressures. We hypothesized that the evolution of the fish immune system and the difference in feeding habits induced the stronger phylosymbiotic signal in the skin. Collectively, this dataset will be useful for understanding the fish microbiome and give insights into phylosymbiosis of aquatic animals across body parts.

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Habitats Show More Impacts Than Host Species in Shaping Gut Microbiota of Sympatric Rodent Species in a Fragmented Forest

Cited by 10 publications

References 76 publications

Species-associated bacterial diversity increases along a gradient of habitat degradation

Species-associated bacterial diversity increases along a gradient of habitat degradation

Effects of forest urbanization on the interplay between small mammal communities and their gut microbiota

Phylosymbiosis in Seven Wild Fish Species Collected Off the Southern Coast of Korea: Skin Microbiome Most Strongly Reflects Evolutionary Pressures

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