Harvard Forest

Data Archive

HF448

Animal Gut Microbiome (AGM) Data from 91 Published Studies for 224 Animal Species

Related Publications

Data

• hf448-01: animal gut microbiome data (preview)

Overview

• Lead: Zhanshan (Sam) Ma, Aaron Ellison
• Investigators:
• Contact: Information Manager
• Start date:
• End date:
• Status: completed
• Location: Global
• Latitude: -90 to +90 degrees
• Longitude: -180 to +180 degrees
• Elevation:
• Datum: WGS84
• Taxa:
• Release date: 2024
• Language: English
• EML file: knb-lter-hfr.448.1
• DOI: digital object identifier
• EDI: data package
• DataONE: data package
• Related links:
• Study type: short-term measurement, modeling
• Research topic: biodiversity studies; ecological informatics and modelling; physiological ecology, population dynamics and species interactions
• LTER core area: population studies
• Keywords: bacteria, communities, genomics, invertebrates, microbes, spatial variability, vertebrates
• Abstract:

  Diversity and heterogeneity often are conflated but are fundamentally different. An aphorism proposed by Shavit and Ellison (2021; J. Phil. 118: 525–548) for distinguishing them is that “a zoo is diverse whereas an ecosystem is heterogeneous.” That is, a zookeeper measuring diversity simply enumerates the different types of animals; interactions are not expected to occur between animals separated by fences or other barriers. In contrast, measures of heterogeneity ought to include both interspecific interactions and relationships between species and their heterogeneous habitats. Here, we use cross-scale, dual scaling-law analyses of heterogeneity and diversity of animal gut microbiomes (AGMs) to address three objectives: (i) estimate the spatial heterogeneity and diversity of animal-gut microbiomes; (ii) analyze influences of phylogeny and diets on scaling of diversity and heterogeneity; (iii) explore mechanistic differences between diversity and heterogeneity in AGMs. From 4903 AGM samples collected from 318 animal species covering all six classes of vertebrates and four major classes of invertebrates, we estimated that ≈640,000 operational taxonomic units (OTUs or “species”) make up the pool of microbial species that could inhabit animal guts, among which ≈8000 are relatively common and ≈800 are dominant. The gut of any single animal, however, includes only 0.01–0.5% of the total species pool. We extended Ma’s diversity-area relationship for scaling diversity and extend Taylor’s Power Law and Luna et al.’s (2020; Diversity 12: 86) interaction diversity for scaling heterogeneity. At the community scale, phylogeny significantly influenced heterogeneity, but diets did not. Phylogeny and diets had limited influence on diversity at both community and landscape scales. Although two common measures of diversity—beta diversity and unevenness—commonly are synonymized with heterogeneity, our data lead us to conclude that diversity and heterogeneity measure two very different properties. Further, differences in scaling of diversity and heterogeneity are a result of heterogeneity being primarily the result of evolved dispersal behavior and interspecific interactions, whereas diversity results from abundances controlled on ecological time scales.

• Methods:

  For more details on methods, please see the associated publication: Ma, ZS and Ellison, AM. Cross-scale scaling-law analyses for the heterogeneity and diversity of animal gut microbiomes from community to landscape. Oikos (in revision).

• Organization: Harvard Forest. 324 North Main Street, Petersham, MA 01366, USA. Phone (978) 724-3302. Fax (978) 724-3595.

• Project: The Harvard Forest Long-Term Ecological Research (LTER) program examines ecological dynamics in the New England region resulting from natural disturbances, environmental change, and human impacts. (ROR).

• Funding: National Science Foundation LTER grants: DEB-8811764, DEB-9411975, DEB-0080592, DEB-0620443, DEB-1237491, DEB-1832210. Other funding: Charles Bullard Fellowship in Forest Research; National Natural Science Foundation of China (No. 72274192).

• Use: This dataset is released to the public under Creative Commons CC0 1.0 (No Rights Reserved). Please keep the dataset creators informed of any plans to use the dataset. Consultation with the original investigators is strongly encouraged. Publications and data products that make use of the dataset should include proper acknowledgement.

• License: Creative Commons Zero v1.0 Universal (CC0-1.0)

• Citation: Ma Z, Ellison A. 2024. Animal Gut Microbiome (AGM) Data from 91 Published Studies for 224 Animal Species. Harvard Forest Data Archive: HF448 (v.1). Environmental Data Initiative: https://doi.org/10.6073/pasta/b4e1b51f686adaee7f637d1b0049be5c.

Detailed Metadata

hf448-01: animal gut microbiome data

1. Study_ID: unique identifier
2. Accession_No: accession number from database where sequence was submitted (see Reference_DOI)
3. Phylum: phylum
4. Class: class
5. Genus: genus
6. Species: species
7. Reference_DOI: full doi for either database accession or associated publication
8. Taxon_age: age in millions of years old; estimated from https://timetree.org/ (unit: dimensionless / missing value: NA)