Diversification of animal gut microbes and NRPS gene clusters in some carnivores, herbivores and omnivores

Guo, Xiurong; Lei, Hui; Zhang, Kailian; Ke, Famin; Song, Can

doi:10.1080/13102818.2020.1835536

Cited by 16 publications

(25 citation statements)

References 24 publications

(34 reference statements)

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“…This might be due to the more complex digestive system of herbivorous species and their dependence on microbes to break down cellulose. This relationship has been shown previously for several species [23,35,39,40,47]. Furthermore, herbivorous mammals are known to rely on microbial metabolic pathways to a greater extent than carnivores [18].…”

Section: Discussionsupporting

confidence: 74%

“…Close similarity in the fecal microbiota of herbivores and great diversity within the carnivores Beside signi cant differences between herbivore and carnivore species, our results reveal a closer similarity in the fecal microbiota of herbivores compared to higher deviations in carnivores. Although there are several studies that describe either a distinct clustering of herbivores and carnivores due to differences in diet or phylogeny or a clustering of herbivorous carnivores to other Carnivora [16, 23,39,40,48], none of them has yet referred to the expansion of these clusters. On the other hand, we found much more indicator species for herbivores than for carnivores and the carnivore indicators are not distributed across all species.…”

Section: Discussionmentioning

confidence: 99%

“…A similar pattern occurs in studies on different tiger and fox subspecies. While about half of the samples in one study [17] consist of Proteobacteria and Fusobacteria respectively, another study found large differences for those microbial families [23]. The abovementioned examples raise the question of whether a minimum number of samples is needed to describe the microbiota of a carnivore species.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Unraveling Differences in Fecal Microbiota Stability in Mammals: From High Variable Carnivores and Consistently Stable Herbivores

Zoelzer

Burger

Dierkes

2021

Preprint

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Background Through the rapid development in third generation sequencing methods and tools, microbiome studies on a various number of species were performed during the last decade. This advance makes it possible to analyze hundreds of samples from different species or animal groups at the same time in order to obtain a general overview of the microbiota. However, there is still uncertainty on the variability of the microbiota of different animal groups and on whether certain bacteria within a species are subject to greater fluctuations than others. This is largely due to the fact that the analysis in most extensive comparative studies is based on only a few samples per species or per study site. In our study, we aim to close this knowledge gap by analyzing multiple individual samples per species from four representative mammalian groups: Ruminantia, Perissodactyla, Canoidea and Feloidea held in different zoos. To assess microbial diversity, 621 fecal samples from 31 species were characterized by sequencing the V3-V4 region of the 16S rRNA gene using Illumina MiSeq. Results We found significant differences in the consistency of microbiota composition and in fecal microbial diversity between carnivore and herbivore species. Whereas the microbiota of carnivores is highly variable and inconsistent within and between species, herbivores show less differences across species boundaries. Furthermore, low-abundant bacterial families show higher fluctuations in the fecal microbiota than high-abundant ones. Conclusions Our data suggest that microbial diversity is significantly higher in herbivores than in carnivores, whereas the microbiota in carnivores, unlike in herbivores, varies widely even within species. This high variability has methodological implications and underlines the need to analyze a minimum amount of samples per species. In our study, we found considerable differences in the occurrence of different bacterial families when looking at just three and six samples. However, from a sample number of 10 onwards, these variations greatly decreased in most cases and led to constant and more reliable results.

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Section: Discussionsupporting

confidence: 74%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Unraveling Differences in Fecal Microbiota Stability in Mammals: From High Variable Carnivores and Consistently Stable Herbivores

Zoelzer

Burger

Dierkes

2021

Preprint

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“…Studies have shown that the gut microbiota of animals are species-specific and have various biological functions, depending on the feeding types of hosts, including herbivores, carnivores, and omnivores ( Gaulke et al, 2018 ; Huang et al, 2020 ; Yukgehnaish et al, 2020 ). Animals with similar feeding habits have a more similar community structure of their intestinal microbiota ( Guo et al, 2020 ), while the composition and functions of gut microbiomes varied among different feeding types ( Liu et al, 2016 ; Wei et al, 2018 ). The results of various feeding types of fish showed that certain energy metabolism pathways were enriched in herbivore/omnivore and zooplanktivore/zoobenthivore fishes, whereas Lipid metabolism and glycan metabolism were enriched in zoobenthivore/piscivore fishes ( Huang et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

“…However, the role of gut microbiota still remains unclear, which hinders the understanding of physiologies, ecologies, and life histories of ophiuroids. In addition, the composition of gut microbiota may have divergences among species with different feeding types ( Guo et al, 2020 ). Some echinoids have evolved gut symbiotic bacteria for acquisition of essential nutrients ( Temara et al, 1993 ; Becker et al, 2009 ).…”

Section: Introductionmentioning

confidence: 99%

Gut Microbial Composition and Diversity in Four Ophiuroid Species: Divergence Between Suspension Feeder and Scavenger and Their Symbiotic Microbes

Dong

et al. 2021

Front. Microbiol.

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Gut microbiota have important roles in the survival and adaptation of the host. Ophiuroids, as the worldwide dominant benthos, have ecological roles in benthic–pelagic coupling in the sea floor. However, little is known about the composition and diversity of their gut microbiota and its potential functions in benthic ecosystems. In present study, we preformed 16S rRNA sequencing and function analysis in four dominant species (Stegophiura sladeni, Ophiopholis mirabilis, Ophiura sarsii vadicola, and Ophiura kinbergi) with two feeding types (suspension feeding/herbivores and scavenger/carnivores) from the Yellow Sea, China. Results showed that 56 phyla and 569 genera of microbiota were identified among ophiuroid guts. Multivariate and diversity analyses showed that the ophiuroid gut microbiota were independent and have higher biodiversity to the sediment microbial in the Yellow Sea. Phyla Proteobacteria, Firmicutes, Tenericutes, and Bacteroidetes were the dominant bacteria, with more than 80% abundance among the four ophiuroid species. A comparison among the gut microbial compositions among four ophiuroids showed the similarity of two offshore carnivore ophiuroids (S. sladeni and O. sarsii vadicola) and variation in the dominant microbiota types of three nearshore ophiuroids (S. sladeni, O. mirabilis, and O. kinbergi). The functional analysis revealed the significant differences of the environment-related expression in S. sladeni gut microbiota between nearshore and offshore environments. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional annotation showed the significant divergence of metabolism pathways between two nearshore species, the herbivores O. mirabilis and carnivores S. sladeni, such as the Lipid metabolism, Carbohydrate metabolism, and Metabolism of cofactors and vitamins. The homolog search and phylogenetic analysis identified the first gut symbiotic Candidatus Hepatoplasma in S. sladeni with important roles for the nutrient metabolisms. Overall, our study reported the comprehensive data of ophiuroid gut microbiota, while the functional microbiome provides insight into the physiology and environmental adaptation in ophiuroids.

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Time series cluster analysis reveals individual assignment of microbiota in captive tiger (Panthera tigris) and wildebeest (Connochaetes taurinus)

Zoelzer

Schneider

Dierkes

2023

Ecology and Evolution

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Fecal microbiota variability and individuality are well studied in humans and also in farm animals (related to diet‐ or disease‐specific influences), but very little is known for exotic zoo‐housed animals. This includes a wide range of species that differ greatly in microbiota composition and variation. For example, herbivorous species show a very similar and constant fecal microbiota over time, whereas carnivorous species appear to be highly variable in fecal microbial diversity and composition. Our objective was to determine whether species‐specific and individual‐specific clustering patterns were observed in the fecal microbiota of wildebeest ( Connochaetes taurinus ) and tigers ( Panthera tigris ). We collected 95 fecal samples of 11 animal individuals that were each sampled over eight consecutive days and analyzed those with Illumina MiSeq sequencing of the V3–V4 region of the 16SrRNA gene. In order to identify species or individual clusters, we applied two different agglomerative hierarchical clustering algorithms – a community detection algorithm and Ward's linkage. Our results showed that both, species‐specific and individual‐specific clustering is possible, but more reliable results were achieved when applying dynamic time warping which finds the optimal alignment between different time series. Furthermore, the bacterial families that distinguish individuals from each other in both species included daily occurring core bacteria (e.g., Acidaminococcaceae in wildebeests or Clostridiaceae in tigers) as well as individual dependent and more fluctuating bacterial families. Our results suggest that while it is necessary to consider multiple consecutive samples per individual, it is then possible to characterize individual abundance patterns in fecal microbiota in both herbivorous and carnivorous species. This would allow establishing individual microbiota profiles of animals housed in zoos, which is a basic prerequisite to quickly detect deviations and use microbiome analysis as a non‐invasive and cost‐effective tool in animal welfare.

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Diversification of animal gut microbes and NRPS gene clusters in some carnivores, herbivores and omnivores

Cited by 16 publications

References 24 publications

Unraveling Differences in Fecal Microbiota Stability in Mammals: From High Variable Carnivores and Consistently Stable Herbivores

Unraveling Differences in Fecal Microbiota Stability in Mammals: From High Variable Carnivores and Consistently Stable Herbivores

Gut Microbial Composition and Diversity in Four Ophiuroid Species: Divergence Between Suspension Feeder and Scavenger and Their Symbiotic Microbes

Time series cluster analysis reveals individual assignment of microbiota in captive tiger (Panthera tigris) and wildebeest (Connochaetes taurinus)

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