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

Zoelzer, Franziska; Schneider, Sebastian; Dierkes, Paul Wilhelm

doi:10.1002/ece3.10066

Cited by 3 publications

(3 citation statements)

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“…Furthermore, it would be interesting to implement time series data for different individuals per species. As we have shown in a previous study, it is possible to identify individuals, that show a very unique microbiota, based on such datasets (Zoelzer et al, 2023). This was possible because of lowabundant bacterial taxa that varied temporarily within and between individuals.…”

Section: Developing a Model To Identify Hostspecific Information From...mentioning

confidence: 94%

Development and evaluation of an ensemble model to identify host-related metadata from fecal microbiota of zoo-housed mammals

Zoelzer,

Monteiro,

Dierkes

2024

Front. Mamm. Sci.

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Much research has been conducted to describe the factors that determine the fecal microbiome, with diet and host phylogeny as the main drivers. The influence of diet has been described at different levels. Firstly, there are major differences in the microbiomes of herbivorous and carnivorous species and secondly the morphology of the digestive system also determines the composition and diversity of the microbiota. In this study, we aim to describe the influence of the three factors – diet, digestive system and host - on the microbiota in order to develop a model that is able to characterize host-specific metadata from an unknown fecal sample. We therefore analyzed the 16s rRNA from 525 fecal samples of 14 zoo-housed species belonging to different phylogenetic groups including herbivores, carnivores and omnivores. We found significant differences in the bacterial taxa correlated with these groups. While herbivores show positive correlations with a large number of bacterial taxa, we found fewer taxa correlating with carnivores or omnivores. We also detected considerable differences in the microbiota of the ruminant, hindgut fermenting and simple digestive system. Based on these results, we developed a logistic ensemble model, that predicts the diet and based on these findings either the herbivorous digestive system or the carnivorous host-family from a given fecal microbiota composition. This model is able to effectively discriminate herbivores, omnivores and carnivores. It also excels at predicting the herbivore-specific digestive system with 98% accuracy, further reinforcing the strong link between microbiota and digestive system morphology. Carnivorous host-family identification achieves an overall accuracy of 79%, although this performance varies between families. We provide this trained model as a tool to enable users to generate host-specific information from their microbiome data. In future research, tools such as the one presented here could lead to a combined approach of microbiome and host-specific analyses which would be a great advantage in non-invasive wildlife monitoring.

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Section: Developing a Model To Identify Hostspecific Information From...mentioning

confidence: 94%

Development and evaluation of an ensemble model to identify host-related metadata from fecal microbiota of zoo-housed mammals

Zoelzer,

Monteiro,

Dierkes

2024

Front. Mamm. Sci.

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Section: Developing a Model To Identify Hostspecific Information From...mentioning

confidence: 94%

Table_2.xlsx

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“…Furthermore, it would be interesting to implement time series data for different individuals per species. As we have shown in a previous study, it is possible to identify individuals, that show a very unique microbiota, based on such datasets (Zoelzer et al, 2023). This was possible because of low-abundant bacterial taxa that varied temporarily within and between individuals.…”

Section: Developing a Model To Identify Host-specific Information Fro...mentioning

confidence: 94%

Characterization of the herbivore and carnivore faecal microbiota with special emphasis on diet and host-specificity

Zölzer

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Research on the human and animal microbiome has become increasingly important in recent years. It is now widely accepted the gut microbiome is of crucial importance to health, as it is involved in a large number of physiological processes. The term ‘microbiome’ refers to the all living microorganisms including their genes and metabolites in a defined environment, while the specific composition of microorganisms consisting of bacteria, archaea and protozoa is referred to as the ‘microbiota’ (Lane-Petter, 1962; Lederberg and McCray, 2001). In recent years, research has focused on various of these communities in the soil (Fierer, 2017), water (Sunagawa et al., 2015), air (Leung et al., 2014) and especially in the human gut. However, this topic is also becoming increasingly relevant for the conservation of endangered species. In the face of global mass extinctions and the listing of over 42,000 animal species as ‘critically endangered’, conservation breeding programmes are more important than ever (Díaz et al., 2019; IUCN, 2022). The responsibility for these tasks lies with zoological institutions, which are dedicated to animal conservation and the continuous monitoring of animal welfare. Microbiome research offers a non-invasive method to support species conservation. By analysing faecal samples, microbial markers can be identified that provide important information about the health status and reproductive cycle of animals (Weingrill et al., 2004; Antwis et al., 2019). Zoological facilities also provide an ideal research environment for comparing individuals from different habitats. In addition, all necessary metadata such as age, sex, kinship or medical treatment are documented and can be used for the analysis. This is the starting point for this thesis. In order to identify such microbial markers, it is necessary to understand the microbiome of a variety of animal species. The first aim is therefore to characterise the faecal microbiota of 31 mammalian species, focusing on herbivores and carnivores. It could be shown that they differ significantly in terms of both microbial diversity and microbiota composition. Herbivorous species express a very diverse microbial composition, consisting mainly of cellulose-degrading taxa of the families Fibrobacteraceae or Spirochaetaceae. In contrast, the microbiota of carnivorous species is less diverse and is dominated by protein-degrading Fusobacteriaceae and Clostridiaceae. In addition, this thesis proves that the microbiota of herbivorous species is highly consistent, whereas the microbiota of carnivorous species is highly variable. The results of this study provide important insights for the sampling scheme of future projects. Especially when analysing carnivorous species, single samples are not sufficient to capture the full variability of the microbiome. These results lead to the question of whether this variability can be explained by daily fluctuations in the individual microbiome and whether this can be used to distinguish between species or individuals. Using individual longitudinal data and a combined approach of clustering algorithms and dynamic time warping, it is shown that such a distinction is possible at the species and individual level. This was confirmed for both a carnivorous (Panthera tigris) and a herbivorous (Connochaetes taurinus) species. These results confirm the influence of the host individual on the faecal microbiota, in addition to the often described influence of diet (Ley et al., 2008a; Kartzinel et al., 2019). Based on the knowledge gained from these studies, a methodology has been developed that will enable the conservation of species in the field to be supported by microbiome research in the future. The focus here lays on the identification of host-specific metadata based on the faecal microbiota. The developed regression model is able to distinguish between carnivorous, herbivorous and omnivorous hosts with up to 99% accuracy. In addition, a more accurate phylogenetic classification of the family (Canidae, Felidae, Ursidae, Herpestidae) can be made for carnivorous hosts. For herbivorous hosts, the model can predict the respective digestive system with up to 100% accuracy, distinguishing between ruminants, hindgut fermenters and a simple digestive system. The acquisition of host-specific metadata from an unknown faecal sample is an important step towards establishing microbiome research in species conservation. Field studies in particular will benefit from such new methods. Usually, costly microsatellite analysis and high-quality host DNA are required to obtain host-specific information from faecal samples. The newly developed method offers a less costly and labour-intensive alternative to conventional techniques and opens up a more accessible field for microbiome research in the field.

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

Cited by 3 publications

References 117 publications

Development and evaluation of an ensemble model to identify host-related metadata from fecal microbiota of zoo-housed mammals

Development and evaluation of an ensemble model to identify host-related metadata from fecal microbiota of zoo-housed mammals

Table_2.xlsx

Characterization of the herbivore and carnivore faecal microbiota with special emphasis on diet and host-specificity

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